- Trackball: Use the X-axis trackball to direct the Catastrofighter (in the shooting stages) and Major Havoc himself (in the platform ones) left and right.
- Fire/Jump Button: Use this button to make the Catastrofighter fire shots (for the shooting stages), and Major Havoc jump up (for the platform ones).
- Shield Button: In the platform stages, you can press and hold this button once for every one of Major Havoc's lives, to activate his shield (which will kill any enemy which touches him with it activated, then immediately deactivate it). Afterwards, this button has no effect for the rest of his current life.
- 1 or 2 Player Buttons: Push these buttons to begin a 1 or 2 player game.
Catastrofighter and Major Havoc
The eponymous Major Havoc (shown in the image to the right) is the protagonist for this game; at the beginning of the game, a player is treated to a short cutscene of him bidding farewell to the five scientists who cloned him and getting into his "Catastrofighter" (shown in the image to the left) then blasting off through a triangular wormhole (after which the first space stage begins). In the space stages, you must direct the Catastrofighter left and right, while firing shots at the attacking Fishoids, Flyboids and Mazoids - and once it has reached the Vaxxian base ship, the stage's remaining time will be awarded to you as bonus points. Major Havoc will then disembark for the first platform stage; in the platform stages, you must direct Havoc through the Vaxxian base ships, following the arrows to their reactors (a radar view of the current one is also displayed at the top of the screen), while avoiding Pyroids and Perkoids. However, one time for every one of Havoc's lives, you may press and hold the Shield Button in these stages to activate his shield, which shall kill any enemy which should touch him with it activated then immediately deactivate it as a result - but it cannot be reactivated again until he loses a life. Once Major Havoc has touched the reactor, he will have to retrace his steps back to the Catastrofighter, before its timer reaches 0; once he has done so, he will receive an "Oxygen Bonus" of 10 x his remaining oxygen level (he can also collect "O²" symbols in these stages in order to increase his oxygen level). Major Havoc shall also receive an extra life at every 100,000 points by default, and every time you clear the Breakout minigame which is seen in the screen's bottom-right corner for a few seconds before each space stage and can also be used to warp to higher stages - however, Atari limited the maximum number of lives that Major Havoc could have at one time to six so if he has six lives and his score reaches a multiple of 100,000 he won't receive a seventh one (but, if he dies just before his score reaches a multiple of 100,000, he can earn one back).
Note: In a two-player game, Major Havoc (and the five scientists he bids farewell to in the opening cutscene) will be coloured as yellow, instead of cyan.
There are five types of enemies in this game; in the space stages, there are Fishoids, which start out blue, are worth 100 points when shot the first time (which also causes them to turn red), and are worth 1000 points when shot the second time (which kills them), along with Flyboids and Mazoids, which are both worth 500 points apiece. However, for the platform stages, there are Pyroids and Perkoids, which are both worth 1000 points apiece - but can only be killed by Major Havoc's shield (which means that after he uses the shield on his current life to kill one of them, the rest shall have to be avoided).